The War Criminal
by holmes-osapien
Summary: Molly/Khan pairing! Tumblr prompt! Molly performs tests on Khan and gets a little too close for comfort.
1. Chapter 1

"Doctor Hooper, do you understand me?" Doctor Leonard 'Bones' McCoy asked the young woman, who stood in front of him. She simply nodded. Bones relaxed his doctor attire, "Molly he can't hurt you, he's held captive in a prison cell." Molly gulped, as she took the syringe, from her commander's out stretched hand. Bones nodded at her, as she left the medical bay, and began her walk across the USS Enterprise. Never in her wildest dreams, had she imagined working as a chief medical officer for star fleet. She had also never foreseen she would be under command of James Kirk. The thought made her extremely nervous; but not nearly as nervous as her current task at hand.

The medical instrument in her small, femine hands, appeared to be engorging in size, and she felt very scared. The Enterprise crew had recently taken custody of the war criminal John Harrison. Only after confrontation with the captain, had his true name and nature been revealed. His name was Khan Noonien Singh. This intriguing man had many remarkable traits, which were unexplainable. That was why she was here, to explain them. She had reached the bridge, and requested permission from her Captain. Jim was perfectly happy for Molly to perform the necessary blood test, only he wished for someone to occupancy her. He volunteered himself as tribute.

The pair entered the lift together, and descended to the holding brig. "How've you been Mols?" Jim asked. She turned to smile at him. They had known each other before either joined star fleet. "I'm great thanks! What's it like being a captain?" She said whilst she nudged him with her elbow. He just laughed, "Well it's not easy being in control all the time." It was her turn to laugh. "I can't imagine why you would find that hard." They made their brisk way to Khan's holding cell. The atmosphere had turned extremely serious, as silence from the cold territory of space, seeped through the walls, and chilled all the bones in Molly's petite body. This was just one of the effects of the war criminal.

Upon reaching the destination of intent, Molly walked over to the glass cell. She bent down to retrieve a peculiar looking circular device and attached it to the glass; all the while she could feel Khan's eyes on her. She failingly tried to concentrate on what she was doing. She gulped as she heard the deep voice of Khan. "More blood tests? I'm starting to think your medical team is inadequate." This made Molly extremely angry, whilst making her bolder. She raised her head from what she was doing to scowl at him. "Who are you to make judgments on inadequacy?" She spat. Khan simply laughed, and moved closer to the glass to stare down the petite woman. "Oh look what we have here! Finally a doctor who's bold enough to talk. One that even talks back." He sneered at her.

She narrowed her eyes, and placed a hand on her hip. "From what I've heard, people should talk back to you more often. It might sometimes shut you up." She snarled back. Khan smirked at her, as he placed his arm though the hole for blood tests, whilst Jim who was still hovering in the background looked quite agape at her abrupt attitude. Molly stabbed the metal syringe into his forearm. "Oh I like you. I think I'll take possession of this one." He proclaimed, speaking more towards Jim than Molly. Jim made a move forward, to say something, before Molly cut him off. "You would be so lucky to have me. I'm a person, not an object do your research, before you come asking after me." She spat. She pulled the syringe firmly from its penetration in his skin. She turned and marched away, flicking her hair out from her collar as she went, fuming from the objectification she had just encountered.

Days passed before Molly was called on to perform more tests on Khan. She quietly accepted her responsibilities and made her way once again to the holding cells. The task the second time around seemed even more daunting as she walked the halls alone. Once she reached the cell, Khan rose to his feet. He stepped towards the glass and stood facing Molly. "Well, I didn't expect to see you again. Though I am rather delighted that I can see you once more." He commented in his dragon like voice. She shivered involuntarily. "Now, now don't be like that. I'm not going to hurt you. I've developed a rather peculiar fascination with you." Molly seemed to think his words were sincere. This is what allowed her to unlock the door and enter the cell. She needed to get closer to him to perform the necessary tests.

Khan watched her like a hawk, analysing her every move as she moved closer. "I'm going to need to take a small sample of your muscle tissue." She whispered nervously. He raised an eyebrow quizzically. "I'll need to take it from your upper arm. Please would you remove your shirt?" She squeaked timidly. She could not understand why she had become such a nervous wreck when she had been so upfront last week. Her body felt like a live wire and his close proximity was definitely the cause. He smirked at her obvious yet strange attraction to him. She herself had not yet realised this fact. But as he pulled off his shirt to reveal his toned chest, she quickly determined what was wrong. 'Oh my lord. I'm attracted to a war criminal' Molly thought repeatedly. She stared a little longer than appropriate at his chest before proceeding to take some of the cells from his bicep.

Khan watched in awe as she worked. Never before had another human taken interest in him this way. He found it curious, yet not unwelcome. Her fingers fluttered over his muscles as she pulled the syringe loose. Before she pulled away Khan grabbed her wrist. She gasped and tried to pull away. "Relax, I'm taking your pulse." He murmured. Her pulse was erratic. He wondered what he could do to elevate it even more. He leaned towards her still taking her pulse. He gently pressed his lips to hers. Molly's pulse rocketed before he pulled away from her completely. She looked completely stunned. Hurriedly she gathered her things and exited the cell before things could become even more insane. "Until the next time Miss Hooper. Or should I say doctor?" He called as she scurried away. For the first time in her life, Molly Hooper didn't know what to do.

FIN. –Jess


	2. Chapter 2

Continuation- I didn't expect people to take interest in this or that people wanted a continuation, but it was requested I do so, so here goes.

She lay awake in bed that night, simply staring up at the ceiling in despair. She could not fathom why her day had progressed as it had done so. What did that kiss mean? Why had he initiated it? What had he meant by it? Question after question swirled around her head in a haze of thick fog, as sleep refused to consume her unless she found answers. Molly couldn't stand the suspense any longer. She leapt from bed and began to dress hastily. She needed to demand answers from him.

...

Khan sat against the wall with impeccable posture. His hands clasped under his chin as he allowed himself to delve into his mind palace. He had accumulated masses of intellect over his three hundred years of existence, yet nothing had prepared him for his current situation. He racked his brains for answers to the inevitable question engraved in neon letters under his eyelids. What were his feelings towards Doctor Hooper? He barely knew her, yet his current existence in this cell revolved around her visits. He knew he liked her that was more than obvious. He had kissed her for heavens sake, that doesn't mean nothing, much to contrary belief. He just wasn't sure to the extent of his feelings.

He was shaken out of his mind palace by the sound of footsteps halting in front of the glass of his cell. Reluctantly, he peeled open his eye lids and turned his head to glare at the incompetent Star fleet crew member. He was surprised to discover that it was not just an insufferable space explorer. It was Doctor Hooper. Her appearance was quite disturbed. Her eyes were sleep deprived and shifted hastily as she stood almost awkwardly in her half dressed state. Strands of her hair sprouted messily around her round and welcoming face. A slight blush travelled across the presumably soft expanse of her delicate skin. Nervously, she ran a slender hand through her hair in attempt to bring order to the untidy strands.

Khan fleeting thought she looked adorable in her semi conscious state, as she fought exhaustion. She would not have dragged herself here unless it was important. He rose steadily to his feet, ignoring the twinge of the stiff muscles in this back. He cautiously approached her. She, in turn, also took a hesitant step forward. Only the thin sheet of reinforced glass stood in their way. Khan held himself straight as he appraised Molly's stature. She sighed and placed a hand on the glass, feeling the cool material beneath her finger tips. "I don't understand." She whispered. He raised his eyebrows. He stared at her hand as confusion flashed across his features. Absently, he placed his hand opposite hers. His hand was far larger than her small one. He wondered how her smooth skin would feel against the rough follicles of his own. Struck with overwhelming compassion he looked down at her form. There was not much of her. Compared to her surroundings, compared to him, she was extremely petite. Such a small person should not occupy such a large amount of space. So why was her being here, in her fragile body, consuming him?

Their eyes locked, as she looked up and he down. Her irises were a deep burnt sienna blended with a full tonal range of russet caramels. Streaks of black shot through the woven shapes of the iris, drawing out the lighter shades. The outer ring was a tawny colour, which contrasted heavily to the sclera. Her eyes were mesmerising, and held an undeniable beauty within the composition. "I don't understand either." Khan replied in a quite voice. Molly's once hard expression soften, and he found himself fascinated by her control over her expression. "I'm not sure I want to." He continued. A flash of emotion, foreign to Khan skimmed her exquisite eyes. "I feel like I know you. I feel like I've known you my entire life. Like I've never known anyone quite extraordinary in the way you are. Yet in reality, I have only known you for an entirely too short period of time. I know nothing about you, I only know of what you have done." Molly whispered.

Khan was utterly astounded by the articulacy of her words. He was fascinated that she had managed to compile into a physical sentences, his own emotions. "You are phenomenal. In three hundred years, I have not met a single living person capable of expressing the majority of my thoughts in a simple phrases. I can assure you, the feeling is mutual. I don't even know your first name." He gushed in his fit of marvel. She smiled shyly at his words and gazed downwards as she hesitantly brushed a stray piece of hair behind her ears. "My name is Molly. Molly Hooper." She breathed. Molly... A simple name. Yet it was alien. A beautiful name for an even more beauteous woman. He saw as Molly blush, deepened in colour and spread down her neck. Realising he must have proclaimed this thought out loud, an array of rouge flushed through his veins also, and broadened lightly across his prominent cheek bones. 


	3. Chapter 3

_Part three: Here we go, the third __and final part of this story!_

Over the past week or two Molly had been secretly retreating to the brig in the dead of night, to sit by Khan as they explored each other's pasts and intellect. Khan and Molly seemed to have forged an unspoken alliance. They had begun to gravitate around and towards each other. Their evolving relationship was like a dance. Choreographed to demonstrate the increasing obsession the man and woman shared for the other. Some nights Molly questioned why she had chosen to allow herself to fall in love with a criminal. The definite heartbreak was certain in the end. In no possible circumstance could they be together. Other nights Khan pondered over why he had let her. It was selfish, and wrong to lead her on. No matter how sincere his feelings were for her, he knew deep down, that he was either going to be killed or held in captivity for the rest of his life. Even if he managed to escape, his existence was purely manufactured to dispose of those not fit enough to live in the world. It was natural selection. But he couldn't allow Molly to venture into the life of exile, no matter how strongly he believed she would comply with his mission.

Khan had planned to escape before he was drawn into an entirely different mission. He stood in the lobby awaiting the hanger door to open, where he and the Captain of the Star ship that had taken him hostage, would ultimately be hurled. Before the destined launch into the void of space, he allowed his thoughts to drift to the one woman he may have been cable of loving with a large part of his chilled heart, if she had not been so cruelly snatched away from him.

It had been the last night they would spend together. He remembered as the tears streamed down her face as he told her what they both knew. It was heart shattering to watch such a delicate woman crumble because of his actions. He hated himself for initiating the brief yet strikingly pleasant kiss all those nights ago. Yet, he could not bring himself to feel guilty, not when he could distinctively remember the jolt of warmth her perfectly smooth and plump lips caused him when they made contact. It tingled his spine to think what could have happened if things had not been different. If only he could have lived and loved in another lifetime, instead of remaining a cold and distant sociopath in a time of war and exploration. This way of life was over complicated. That's why his task as a superior human was to wipe out the painstaking existence of a lower form. Khan emptied his mind of all the repulsive thoughts of weakness as he narrowed his mind to what he had to do. Molly would have to be forgotten.

…

Molly could barely contain a stifling sob as she stood watching the man she had handed her heart to. Across the communication device between Star ships, she saw as Khan fought his way to dominance. He conversed briefly with the first Officer Spock, demanding the exchange of his frozen crewmembers. Surprisingly to many members of the crew, Spock complied. Molly felt disgusted with herself, as she knew exactly what Spock's plan of action was. She had of course helped remove Khan's beloved from the insides of the torpedo's. Khan's words at this point truly frightened her. If he went through with his plans to suffocate her crew, she would be among those murdered. She watched in anticipation as the three hostages from her own crew were beamed back aboard the USS Enterprise. A smirk crawled its way across Khan handsome features as what he believed to be his crew materialized in the largest hanger bay of the USS Vengeance. Her heart plummeted as Khan's words rang through the halls of the enterprise. "After all, no ship should go down without her Captain."

The ship was targeted and all hell broke loose. In the heat of the moment, Spock ordered the torpedo's to implode. Moll had to cover her mouth in attempt not to scream as the USS Vengeance plummeted through the vacuum of space. There was no possible way an ordinary man could survive a fall like that. But Khan was no ordinary man. The main power grid unexpectedly cut out. Their own ship began to fall nose first from orbit. Molly dropped into the nearest seat and began to help try and repower the ship.

Time appeared to slow down as every man, woman and child fell through the atmosphere, towards an imminent and prominent death. No one knew that the reason the ship was suddenly revived, as a result of Jim sacrificing his life in order to save his crew. Not until Spock ran from the bridge and sped to the entrance of the warp core. Both Molly and Nyota ran after him, arriving in time to watch the heart wrenching exchange between the friends, before the radiation poisoning consumed their captain and friend. Both women withheld tears as Spock screamed Khan's name in anger. The three of them ran back to the bridge, just in time to for the enemy ship to soar past them.

Molly watched the monitor in hope as they searched the ships wreckage for signs of life. She knew it was wrong to pine after the man who had killed Jim. But she unconditionally and erratically loved Khan, no matter how terrible his actions were. She could cope if he was held prisoner, not if he was killed however. She headed back to the medical bay to assist the medical team. Once there, Jim's body was brought in. Her already tattered heart shattered at Jim's last painstaking expression. She dropped into the desk chair and dropped her head into her arms resting on the desk.

Quite unexpectedly something nudged the side of her head and made a gurgling noise. She slowly raised her head to look at the creature that had disturbed her. Her gasp was extremely audible as she sat up straight to inspect the once-dead tribble. "BONES!" She nearly screamed. At first he didn't respond, from being too wrapped up in his grief. But after she yelled his nickname twice more, he turned to stare at her without expression. His eyes were dead. She looked down at the very much alive tribble. When it was deceased, she had injected it with a small dose of Khan's blood platelets to she why they had a regenerative quality. She did not know how or why the dose had brought the animal back to life. She only knew that she had nothing to lose. "I can save Jim." She whispered. A few members of the crew still in the medical bay, turned to stare at her disbelievingly. "I can save him!" Molly said louder this time. With this proclamation she leapt into action. "I need a cryo tube!" She shrieked, running to the nearest tube. "Bones remove this man from the container, but keep him in a induced coma." Bones looked skeptical. "Have you lost your mind?" He asked. "Quite possibly!" She shrieked as she ran to the cold incubator. "There's no blood left!" She froze. The only way she was going to have even a remote chance of saving Jim was by occupying more blood from Khan. She knew what she had to do.

…

Molly ran as fast as her legs would carry her. She sprinted with the upmost determination, which she had ever possessed in her lifetime. Upon reaching the transporter room, she persuaded the man in charge to beam her to the exact location Khan and Spock were battling. When her scrambled particles reformed, she found herself on the outside of a moving ship. The wind lashed her disheveled hair around her face. In order to see properly she had to squint down at her first officer, who was currently strangling Khan. "STOP!" She screamed above the wind. Neither man stopped wrestling. "PLEASE! I CAN SAVE HIM! I CAN SAVE JIM!" She shrieked.

Spock froze, whilst holding Khan in a chokehold. Spock suddenly turned the tables and pinned Khan to the metal beneath their feet. He looked as if he was about to render Khan unconscious. That was until Molly lunged forward and caught his wrist. He glared at her in disgust, his nostrils flaring. Instead, she pushed him away from Khan altogether. To prevent Khan from attempting to escape again, she sat on his chest. Khan struggled as much as he could, but he was extremely reluctant to harm her in anyway. "Molly. Get off of me. I don't want to hurt you." He hissed in such away that the pointy-eared elf couldn't hear him. Molly leaned over him and pushed his face to the side to allow her better access to his neck. A curtain of her long hair falling forward and blocking Spock's view hid her actions. "Shut up. You have to trust me." As gently as she could she dosed him with a syringe containing sedatives strong enough to knock him out for 48 hours.

His body went limb as the induced drugs surged through his veins, whilst his eyelids drooped unconsciously, covering his vibrantly coloured irises. She watched as his psychotic persona faded with his awareness, and a façade of innocence seeped across his drowsy features. She pushed herself up to a standing position and faced the commander. "I'm sorry but I need him back aboard the enterprise, with minimal damage. It's the only way I have a slight chance of reviving the captain." She explained. He said nothing to her, but pulled out his communicator. "Beam all three of us up Scotty."

…

Two weeks it had taken. Two entire weeks Molly had been in the surgery room, performing acts that should have been scripted from Frankenstein. Jim's cells had been heavily irradiated, even with Khan's 'miracle' blood the process or reforming cells had taken its time. His heart had started almost immediately, but with each new dose of platelets, he suffered cardiac arrest. Molly felt the absolute need to stay in the same place constantly monitoring Jim and Khan, lying adjacently in similarly induced comas. Over this period of time Molly had time to think, to plan. She had everything copulated in her mind. She was ready to act on it at any given moment.

When Jim finally woke up, he extremely disorientated, as was to be expected. After Jim was back on his feet, Molly went about her plans involving Khan. She was in charge of Khan's cryogenic incarceration. She and the other doctors guarded by the security team, escorted Khan's cryo tube to the black box, which currently stored the other members of Khan's crew. She made sure she was the last to leave. In her few moments alone, she quickly tampered with his container. Setting about making sure he had thawed in time, she injected him a penultimate time; this injection to comatose him, and then a final injection, when the time came, to wake him from the dreamless sleep.

FIN. –Jess

_Epilogue_

_She waited as long as she deemed necessary. When the need arose she could be extremely patient. Silently she slipped into the black box, a single syringe held in her small hand. Molly pressed the release button on the cryo tube. With a cloud of mist, Khan slid from the tube on a panel. She slid the needle into the side of his neck and pressed the pale green solution into his bloodstream. A few moments passed before Khan drew an icy breath. His eyes fluttered open and locked with Molly__'__s. Cautiously he sat up and took in his surroundings. __"__You__'__ve been a naughty girl.__"__ He taunted. Molly__'__s expression hardened. __"__Give up your mission. Stop this homicidal madness, and I__'__ll run away with you. Spend the rest of my life with you.__"__ He chuckled quietly and rose to his feet. He pressed their bodies together. __"__I never wanted to become a murderer. I had no way of escape. Not until you offered it to me. For that I thank you Molly Hooper. You are the one woman who matters the most.__"__ With this she seized his lips, as well as his heart. _


End file.
